Monthly Archives: December 2015

American Gut News & Updates: Building Macro Data from Microbiomes

Some people never struggle with their weight. Other people seem to gain a pound just by thinking of cheesecake, but they never get a mosquito bite. Or they can’t metabolize certain antibiotics – or over-the-counter painkillers. While it’s tempting to blame our genes for everything, we shouldn’t.

According to Rob Knight, co-founder and lead investigator of Open Humans Research Partner American Gut, maybe we should blame – or thank – our microbiome!

American Gut is the world’s largest open-source, crowdfunded science project. Its objective is to study certain microbes and learn how they impact disease, wellness, and even human behavior. Microbes are the tiny organisms that live in and on our bodies (plus everywhere else). They’re much more plentiful and variable than our DNA, and researchers are discovering that they play a huge part in our resistance to — and our resilience from — numerous health issues, including asthma, rheumatoid arthritis and cardiovascular disease. It’s the cutting edge of research, and could be a strange-but-cool gift if you’re still looking for something special.

American Gut participants have the opportunity to find out what’s lurking in your gut, mouth, and on your skin by using a sample kit that you purchase for $99. These contributions allow Rob Knight and his team to study the relationship between people’s health, habits and their microbial diversity. There’s tremendous statistical power in a study with a population sample in the thousands, and, in just 3 years, American Gut has amassed a participant base of over 10,000 people!

One big change for American Gut this year is that it moved from the University of Colorado at Boulder to the University of California at San Diego. Dr. Knight wanted to bring his lab closer to the San Diego Supercomputer Center and the Scripps Research Institute since analyzing microbiomes requires state of the art computation and bioinformatics. Being in California also provides the opportunity to collaborate with different investigators.

In October, Dr. Knight and his researchers celebrated the fact that American Gut has now received over $1 million in donations. This is a huge accomplishment for any research study, and especially one that asks participants to collect their own samples!

Additionally, the American Gut team has been making plans to expand internationally.Since they already have sister projects in Australia and Britain, we’re excited to find out where they head to next. But don’t think that you have to wait to tell your friends overseas: American Gut is the only Open Humans Research Partner that accepts international participants. It also accepts samples from most pets, in case any of you are curious about how your gut microbiome compares to your dog or cat’s!

To date, American Gut has released the de-identified data from ~7000 sample kits, and the number of participants continues to grow!If you want to learn more about the project, check out this recent Quantified Body podcast with Rob Knight or his TED Talk from early last year.

So, if you’re struggling with what to give your health-conscious or scientifically-curious friends and loved ones this season, consider gifting an American Gut kit! It allows people who think they know everything about themselves to learn just a little bit more. Plus, they get to make a contribution to science! What could be better than that?


What We’re Reading

Harvard PGP data in Action!

As an Open Humans member, we wanted to share some news and updates from one of our partner studies – the Harvard Personal Genome Project!

About Harvard PGP

The Harvard Personal Genome Project (or PGP) is, in many ways, the spiritual parent of the Open Humans project. The PGP began in 2005 with a proposal by George Church. Its mission is to advance personal genomic research – the study of everything in our DNA – through public data sharing. It hosts genomic and health data from thousands of participants who understand that their data, by its very nature, is potentially identifiable.

Interested in participating? You can sign up here:

Breaking the $1000 genome barrier!

This fall, Veritas debuted an offer for $1000 genome sequencing exclusive to Harvard PGP participants! The PGP’s resources are limited, and it has many more volunteers than it can sequence at the moment. Now participants have a faster way to get their genome in the hands of researchers: By getting a genome through Veritas, then donating it to the PGP and/or Open Humans.

Data visualization

Earlier this year, Abram Connelly developed an interactive tool called “Untap” to explore Harvard PGP data. Abram is a PGP participant, a member of the PGP staff, and a researcher at Curoverse, and he wanted to make the PGP data more accessible to all. His coworker Nancy Ouyang, also a PGP staff member, wrote a great summary of using Untap for the blog.

Genome interpretation

A community of genomic researchers called the Critical Assessment of Genome Interpretation (or “CAGI”) launched an experiment using PGP data. This experiment challenges researchers to match PGP participant genomes to health and trait profiles. The challenge is open until December 7th. CAGI is a great match for PGP data because the methods can be “open source”: both algorithms and data can be completely open and available to all.

Celebrating 10 years at GET

The PGP celebrated its 10th anniversary in September at the GET Global Conference in Vienna, Austria. “GET” stands for “Genomes Environments and Traits”, and the conferences are traditionally very participant-centric: the GET Labs events invite attendees to work with other research groups and were an inspiration for Open Humans. In 2015, GET went farther afield and was hosted by a PGP member site (Genom Austria), reaching out to the global community. Open Humans’ co-founder Madeleine Ball also spoke about data access and sharing as part of the session on Society. We’re looking forward to meeting participants – and Open Humans members – at the next GET Conference in Boston, in April 2016.